Align D-xylonate dehydratase subunit (EC 4.2.1.25; EC 4.2.1.82) (characterized)
to candidate WP_007690272.1 C447_RS01785 galactonate dehydratase
Query= metacyc::MONOMER-18070 (393 letters) >NCBI__GCF_000336675.1:WP_007690272.1 Length = 384 Score = 199 bits (507), Expect = 9e-56 Identities = 130/390 (33%), Positives = 210/390 (53%), Gaps = 22/390 (5%) Query: 1 MTKISEIEAYILGKEVTSAQWASLMVLVRVTTNDGRVGWGETVSALRAEAVANFVKKI-N 59 MT+I + E Y + +W + + + T+DG VGWGE V R++ VA V+++ + Sbjct: 1 MTEIVDYELYDV-----PPRW----LFLELETSDGLVGWGEPVVEGRSKTVAAAVEELLD 51 Query: 60 TVLKGNDVFNVEKNRLEWYKHDFNMTISLESTTAYSAVDIASWDIIGKELGAPLYKLLGG 119 L G D +E + Y+ F + +A + +D A WDI GK GAP+++LLGG Sbjct: 52 NYLLGRDPNRIEDHWQAMYRGGFYRGGPI-LMSAIAGIDQALWDIKGKRFGAPVHELLGG 110 Query: 120 KTRDKVLVYANGWYQNCVKPEDFAEKAKEIVKMGYKALKFDPFGPYFNDISKKGLDIAEE 179 + RD++ VY W +P D E A E V+ G+ ALK + S ++ A E Sbjct: 111 RARDRIRVYQ--WIGGD-RPADVGEAAAEQVEAGFSALKMNATPEIRRVDSPAAVEAAVE 167 Query: 180 RVKAVREAVGDNVDILIEHHGRFNANSAIMIAKRLEKYNPLFMEEPIHPEDVEGLRKYRN 239 R+++VREAVG V+I ++ HGR A + LE + P+F+EEP+ P+ + L + + Sbjct: 168 RLRSVREAVGPEVEIGVDFHGRVTKPMAKRLVAALEPHEPMFVEEPVLPQHNDALAEIAS 227 Query: 240 NTSLRIALGERIINKQQALYFMKEGLVDFLQADLYRIGGVTETKKVVGIAETFDVQMAFH 299 +T+ IA GER+ ++ ++G VD +Q DL GG+TE KK+ +AE +DV +A H Sbjct: 228 HTTTPIATGERMFSRWDYKEVFEDGTVDVIQPDLSHAGGITEVKKIAAMAEAYDVALAPH 287 Query: 300 NAQGPILNAVTLQFDAFIPNFLIQE-SFYDWFPSWKRELIYNGTP----IDNGYAIIPER 354 GP+ A +Q DA PN LIQE S + L Y P ++G+ + + Sbjct: 288 CPLGPVALASCIQVDACSPNALIQEQSLNIHYNETSDVLDYLADPSVFEYEDGFVDVLDE 347 Query: 355 PGLGVEVNEKMLDSLKVKGEEYFNPEEPVW 384 PGLG++++E+ +++ + EE + P+W Sbjct: 348 PGLGIDLDEEYIEA---QSEEPVDWHNPIW 374 Lambda K H 0.319 0.137 0.409 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 388 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 393 Length of database: 384 Length adjustment: 30 Effective length of query: 363 Effective length of database: 354 Effective search space: 128502 Effective search space used: 128502 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory